Dictionaries GENOME 559: Introduction to Statistical and Computational Genomics Prof. William Stafford Noble

Dictionaries A dictionary organizes linked information. Examples: - word and definition - name and phone number - name and DNA sequence - username and password If you know the first entry, you can quickly and easily get the second one. Accessing a dict entry is fast, but not quite as fast as indexing in a list or string.

Rules for dictionaries The first item is a key. Each key can appear only once in a dict. A key must be an immutable object: number, string, or tuple. Lists cannot be keys (they are mutable). The key is the item you'll use to do look-ups. Each key is paired with a value.

Key examples Phone book: we have a name, we want a number Name is the key, number is the value Crank call prevention: we have a number, we want a name Number is the key, name is the value

Creating a dictionary #create an empty dictionary myDict = {} #create a dictionary with three entries myDict = {"Curly":4123, "Larry":2057, "Moe":1122} #add another entry myDict["Shemp"] = 2232 #change Moe's phone number myDict["Moe"] = 4040 #delete Moe from dictionary del myDict["Moe"]

Using a dictionary >>> myDict = {"Curly":4123, "Larry":2057, "Moe":1122} >>> myDict["Moe"] 1122 >>> myDict.keys() ['Larry', 'Moe', 'Curly'] >>> "Curly" in myDict True >>> "curly" in myDict False >>> myDict.values() [2057, 1122, 4123] >>> len(myDict) 3 get all the keys as a list the keys are not in any particular order! curly is not the same as Curly get all the values as a list the number of key:value pairs

Making a useful dictionary Suppose we have a file that gives the alignment score for a large number of sequences: seq1 <tab> 37 seq2 <tab> 182 etc. import sys openFile = open(sys.argv[1], "r") scoreDict = {} for line in openFile: fields = line.strip().split("\t") scoreDict[fields[0]] = float(fields[1]) myFile.close() we now have a dictionary where we can look up a score for any name

Traversing a dictionary by key # birthdays is a dictionary with names as keys # and birth dates as values for person in birthdays.keys(): print "Send", person, "a card on", birthdays[person]

Sorting a dictionary by key # birthdays is a dictionary with names as keys # and birth dates as values bkeys = birthdays.keys() # birthday is a dictionary bkeys.sort() for person in bkeys: print "Send", person, "a card on", birthdays[person] Uses the list.sort() method - if the list contains strings, they will be sorted alphanumerically

dictionary basics D = {'dna':'T','rna':'U'} # dictionary literal assignment D = {} # make an empty dictionary D.keys() # get the keys as a list D.values() # get the values as a list D['dna'] # get a value based on key D['dna'] = 'T' # set a key:value pair del D['dna'] # delete a key:value pair 'dna' in D # True if key 'dna' is found in D, else False The keys must be immutable objects (e.g. string, int, tuple). The values can be anything (including a list or another dictionary). The order of elements in the list returned by D.keys() or D.values() is arbitrary (effectively random). Each key can be stored only once in the dictionary, so if you set the value for a key for a second time it OVERWRITES the old value!

File format: seq1 <tab> score seq2 <tab> score etc. Sample problem #1 The file ‘small-scores.txt’ contains scores assigned to many different sequences. Write a program find- best-score.py that prints each sequence next to the square of its associated value. $ python print-squares.py small-scores.txt AGGSIIR 0.000376361 AGGSIIR 0.0662605 IALKPK 1.64762 IALKPK 0.000906147 AGGSIIR 0.00154437 NPIDVK 0.34584 IALKPK 0.224348 NPIDVK 0.0187335 IALKPK 0.00124857

Solution #1 import sys # Open the file for reading. in_file_name = sys.argv[1] in_file = open(in_file_name, "r") # Read each line and print the square. for line in in_file: words = line.rstrip().split("\t") score = float(words[0]) sequence = words[1] print "%s\t%g" % (sequence, score * score) in_file.close()

Sample problem #2 Write a program find-best-score.py that prints the maximal score assigned to each sequence. You can also run it on small-scores.txt and large-scores.txt. $ python find-best-score.py small-scores.txt IALKPK 1.2836 AGGSIIR 0.257411 NPIDVK 0.588082

import sys # Open the file for reading. in_file_name = sys import sys # Open the file for reading. in_file_name = sys.argv[1] in_file = open(in_file_name, "r") # Set up a dictionary. best_score = {} # Key = sequence, value = score for line in in_file: words = line.rstrip().split("\t") score = float(words[0]) sequence = words[1] if ( (not sequence in best_score) or (score > best_score[sequence]) ): best_score[sequence] = score in_file.close() for sequence in best_score.keys(): print "%s\t%g" % (sequence, best_score[sequence]) Solution #2

Sample problem #3 The file ”unique-scores.txt" contains blastn scores for a large number of sequences with a particular query. Write a program that reads them into a dictionary, sorts them by sequence name, and prints them. >python sort_dict.py scores.txt seq00000 293 seq00001 315 seq00002 556 seq00003 556 seq00004 617 seq00005 158 etc.

Solution #3 import sys myFile = open(sys.argv[1], "r") # make an empty dictionary and populate it scoreDict = {} for line in myFile: fields = line.strip().split("\t") # record each value with name as key scoreDict[fields[0]] = float(fields[1]) myFile.close() # get key list and sort it keys = scoreDict.keys() keys.sort() # print based on sorted keys for key in keys: print key + "\t" + str(scoreDict[key])

Sample problem #4 Suppose you have a list of sequence names whose scores you are interested in extracting from the large list of scores (in the same file ”unique-scores.txt"). Modify your previous program to read a list of sequence names from a second file and print the scores for just those sequences. A sample "seq-names.txt" is linked from the web site. >python get_scores.py scores.txt seq-names.txt seq00036 784 seq57157 523 seq58039 517 seq67160 641 seq76732 44 seq83199 440 seq92309 446

these two code segments can be in either order Solution #4 import sys # get a list of the names of interest seqNameFile = open(sys.argv[2], "r") seqNameList = [] for line in seqNameFile: seqNameList.append(line.strip()) seqNameFile.close() # make a dictionary of the scores, keyed on name dictFile = open(sys.argv[1], "r") scoreDict = {} for line in dictFile: fields = line.strip().split("\t") scoreDict[fields[0]] = int(fields[1]) dictFile.close() # finally, use the dictionary for seqName in seqNameList: print seqName + "\t" + str(scoreDict[seqName]) these two code segments can be in either order

Challenge problems 1. Extend your program in sample problem 2 so that it gives useful user feedback when a sequence name is missing from the dictionary. 2. Sort the list of scores in the same file (scores.txt) by score, with the highest scoring first. Print the sequence name and its score in that order. You can do this using a dictionary (ignore the fact that more than one sequence may have the same score, so some may get lost).

Challenge 1 solution import sys # get a list of the names of interest seqNameFile = open(sys.argv[2], "r") seqNameList = [] for line in seqNameFile: seqNameList.append(line.strip()) seqNameFile.close() # make a dictionary of the scores, keyed on name dictFile = open(sys.argv[1], "r") scoreDict = {} for line in dictFile: fields = line.strip().split("\t") scoreDict[fields[0]] = int(fields[1]) dictFile.close() # finally, use the dictionary for seqName in seqNameList: if not seqName in scoreDict: print seqName, "not found" else: print seqName + "\t" + scoreDict[seqName]

Challenge 2 solution import sys dictFile = open(sys.argv[1], "r") scoreDict = {} for line in dictFile: fields = line.strip().split("\t") scoreDict[int(fields[1])] = fields[0] dictFile.close() sortKeys = scoreDict.keys() sortKeys.sort() sortKeys.reverse() # sort makes ascending sort for numbers for key in sortKeys: print scoreDict[key] + "\t" + key